This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The conformational heterogeneity in nucleic acids is implied by the complex and rugged energy landscape of nucleic acids, which controls their folding and function. Moreover, there is increased evidence of heterogeneity in transient intermediates as well as the final folded state of proteins and structured RNAs. Despite the fundamental importance of conformational heterogeneity in nucleic acids, it has not been properly studied due to a lack of suitable experimental techniques. A newly developed Au-SAXS-based x-ray ruler provides the distance probability distribution of an ensemble of molecules. This technique provides a unique and powerful probe of macromolecular conformational heterogeneity. We propose to study the conformational flexibility and heterogeneity of modular DNA and RNA structures, including A-tract, bulges, single-stranded and double stranded junctions and simple functional RNA structure such as the HIV TAR RNA. We intend to measure the conformational distributions and heterogeneity in these nucleic acids structures and relate the distributions to nucleic acid folding and function.